pretextMap_scaffolding.pbs

#!/bin/bash
#PBS -q bigmem
#PBS -l select=1:ncpus=64:mem=250GB
#PBS -l walltime=168:00:00
#PBS -W group_list=x-ccast-prj-hulke
#PBS -N ContactMatrixWithPretextScaffolding


cd /mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/HifiOmniCAssembly

source /mmfs1/home/senta.kryzer/miniconda3/bin/activate pretextmap_env

module load samtools 

samtools view -h ./alignment_scaffolding/mapped_omnic_scaffolding.PT.bam | PretextMap -o map_omnic_pretext_scaffolding --sortby nosort --mapq 10